There's a good column in the New Republic this week noting the irony that John Roberts decided to uphold the individual insurance requirement but struck down the expansion of state Medicaid payments. Part of the Affordable Care Act would have required states to expand Medicaid eligibility if they wanted to receive increased federal funding. They would have had to pick up a relatively small amount of the increase (10%) in return for big bucks from the federal government, but the court still struck it down.
The statement made by the court in this decision essentially opens the door for states to fight any future changes that congress makes to Medicaid. And this presents significant challenges for the federal government as it seeks to protect the viability of its investment now and in the future. If the states begin to exercise too much individual control over the program, the federal government may opt to back off and simply run the entire program at the federal level. Something that, ironically, Democrats would prefer.

It'd be ironic if a precedent set by the conservatives in a contentious healthcare debate ultimately leads to a more centralized government program.